The Obama administration lobbied Australia to change its asylum seeker policy, actively disagreeing with the Australia's off-shore detention and "Stop the Boats" mentality.

Former deputy secretary of state Heather Higginbottom has given an insight into how the secretive refugee-swap deal between the two allies came about, while revealing the United States, under former president Barack Obama, wanted to "bring relief" to asylum seekers held on Nauru and Manus Island.

Former US President Barack Obama did not agree with Australia's asylum seeker policy, according to a former Deputy Secretary of State who worked in his administration. Photo: Pablo Martinez Monsivais

The deal was the subject of a tense first phone call between President Donald Trump and Prime Minister Malcolm Turnbull, with Mr Trump labelling it "stupid", "rotten", "horrible" and "disgusting".

But Ms Higginbottom, writing for Time magazine, said it was struck with humanitarian solutions in mind, by an administration uncomfortable with Australia's stance.

"While the last administration strongly pressed the Australian government to change its policy toward asylum seekers, we also sought to immediately relieve the suffering of these refugees and agreed to resettle up to 1200 after they went through the US government's rigorous refugee screening processes," Ms Higginbottom, who now serves as the chief operating officer of CARE, wrote.

"We also made clear that while we disagreed with their policy of detention, Australia is a critical ally, particularly in the Pacific, and a leader in humanitarian assistance and refugee resettlement globally.

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"I only know all this because of my former role as deputy secretary of state, not because of anything I am reading in the newspapers or watching on television, and that's part of the problem. If we don't even discuss the underlying facts of international debates and disagreements, how are we ever going to build anything resembling consensus to address them?"

Immigration Minister Peter Dutton's office did not respond to requests for comment.

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The United Nations refugee agency has repeatedly criticised Australia's policy, but Ms Higginbottom's comments are the first to reveal the United States had also drawn issue with it.

In contrast to Mr Turnbull, who, in a leaked transcript of his conversation with Mr Trump called the asylum seekers "economic refugees", Ms Higginbottom, who said she was the Obama administration official responsible for negotiating the agreement with Australia, had a different view.

"These are people who risked their lives on makeshift boats to flee conflict and the lack of access top basic means of survival, but were turned back by an Australia government that refuses asylum seekers who arrive by sea," she said.

"As we fuss and fret over the clash of presidential and prime ministerial personalities, actual human beings suffer."

In speaking to Mr Trump, Mr Turnbull admitted "the only reason we cannot let them into Australia is because of our commitment to not allow people to come by boat".

"Otherwise we would have let them in. If they had arrived by airplane and with a tourist visa then they would be here," he said.

In return for the United States agreeing to vet up to 1250 asylum seekers in Australia's detention centres, with the "good faith" agreement that those who passed would be accepted, Australia will accept Central American refugees the United States can't settle.

"Basically, we are taking people from the previous administration that they were very keen on getting out of the United States," Mr Turnbull told Mr Trump.

"We will take more. We will take anyone that you want us to take. The only people that we do not take are people who come by boat. So we would rather take a not very attractive guy that help you out then to take a Noble [sic] Peace Prize winner that comes by boat. That is the point."

Australia remains at the mercy of the United States timetable for processing the asylum seekers, with Mr Trump's decision to slash his nation's overall annual refugee intake from 110,000 to 50,000, a quota they have already reached.

Mr Dutton said with the American year finishing on September 30, Australia's agreement had "now been pushed into October in terms of when people will move", but last month he told Sky News he remained confident the Manus Island centre would close by the end of October.